Improve collection table functionality

mobie · Jul 18, 2024 · ba5ab6f · ba5ab6f
1 parent ebdc03e
commit ba5ab6f
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Showing 107 changed files with 199 additions and 159 deletions.
diff --git a/.gitignore b/.gitignore
@@ -17,7 +17,7 @@ hs_err_*.log
 
 pom.xml.releaseBackup
 
-src/test/java/projects
+src/test/java/projects/
 
 
 mobie-files

diff --git a/pom.xml b/pom.xml
@@ -9,7 +9,7 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>5.2.4-SNAPSHOT</version>
+    <version>5.3.0-SNAPSHOT</version>
 
     <!-- mvn clean install -Dmaven.test.skip=true -Dscijava.app.directory=/Users/tischer/Desktop/Fiji/Fiji-MoBIE.app -->
 
@@ -84,7 +84,7 @@
         <license.copyrightOwners>EMBL</license.copyrightOwners>
         <enforcer.skip>true</enforcer.skip>
 
-        <mobie-io.version>3.0.2</mobie-io.version>
+        <mobie-io.version>3.0.3</mobie-io.version>
         <imagej-utils.version>0.7.0</imagej-utils.version>
 
         <bigdataviewer-playground.version>0.9.0</bigdataviewer-playground.version>

diff --git a/src/main/java/org/embl/mobie/MoBIE.java b/src/main/java/org/embl/mobie/MoBIE.java
@@ -120,7 +120,7 @@ public MoBIE( String uri, MoBIESettings settings ) throws IOException
 			initImageJAndMoBIE();
 			initProject( IOHelper.getFileName( uri ) );
 
-			CollectionTableDataSetter dataSetter = new CollectionTableDataSetter( table );
+			CollectionTableDataSetter dataSetter = new CollectionTableDataSetter( table, settings.values.getDataRoot() );
 			dataSetter.addToDataset( dataset );
 			dataset.is2D( false ); // TODO: determine from data?!
 

diff --git a/src/main/java/org/embl/mobie/MoBIESettings.java b/src/main/java/org/embl/mobie/MoBIESettings.java
@@ -108,12 +108,6 @@ public MoBIESettings setVoxelDimensions( VoxelDimensions voxelDimensions )
 		return this;
 	}
 
-	public MoBIESettings appendGroovyCode( String groovyCode )
-	{
-		this.values.groovyScript += groovyCode;
-		return this;
-	}
-
 	public MoBIESettings openedFromCLI( Boolean cli )
 	{
 		this.values.openedFromCLI = cli;
@@ -126,6 +120,12 @@ public MoBIESettings projectType( ProjectType projectType )
 		return this;
 	}
 
+	public MoBIESettings dataRoot( String dataRoot )
+	{
+		this.values.dataRoot = dataRoot;
+		return this;
+	}
+
 
 	public static class Values
 	{
@@ -141,7 +141,12 @@ public static class Values
 		private VoxelDimensions voxelDimensions = null;
 		private Boolean openedFromCLI = false; // started from CLI
 		private ProjectType projectType = ProjectType.MoBIEJSON;
-		private String groovyScript = "";
+		private String dataRoot = null;
+
+		public String getDataRoot()
+		{
+			return dataRoot;
+		}
 
 		public VoxelDimensions getVoxelDimensions()
 		{

diff --git a/src/main/java/org/embl/mobie/cmd/ProjectCmd.java b/src/main/java/org/embl/mobie/cmd/ProjectCmd.java
@@ -28,7 +28,6 @@
  */
 package org.embl.mobie.cmd;
 
-import net.imagej.ImageJ;
 import org.embl.mobie.MoBIE;
 import org.embl.mobie.MoBIESettings;
 import picocli.CommandLine;

diff --git a/src/main/java/org/embl/mobie/command/open/OpenCollectionTableCommand.java b/src/main/java/org/embl/mobie/command/open/OpenCollectionTableCommand.java
@@ -33,19 +33,13 @@
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.ProjectType;
 import org.embl.mobie.command.CommandConstants;
-import org.embl.mobie.command.SpatialCalibration;
 import org.embl.mobie.lib.MoBIEHelper;
-import org.embl.mobie.lib.transform.GridType;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 
 import java.io.File;
 import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.stream.Collectors;
 
 @Plugin(type = Command.class, menuPath = CommandConstants.MOBIE_PLUGIN_OPEN + "Open Collection Table..." )
 public class OpenCollectionTableCommand implements Command {
@@ -55,16 +49,24 @@ public class OpenCollectionTableCommand implements Command {
 	@Parameter( label = "Table Path", required = true )
 	public File table;
 
+	@Parameter( label = "Data Root Folder",
+			style = "directory",
+			description = "Use this is if the paths to the images and labels in the table are relative.",
+			required = false )
+	public File dataRoot;
+
 	@Override
 	public void run()
 	{
 		DebugTools.setRootLevel( "OFF" );
 
 		final MoBIESettings settings = new MoBIESettings()
-				.projectType( ProjectType.CollectionTable );
+				.projectType( ProjectType.CollectionTable )
+				.dataRoot( dataRoot.getAbsolutePath() );
 
 		try
 		{
+			String rootPath = dataRoot == null ? null : dataRoot.getAbsolutePath();
 			new MoBIE( MoBIEHelper.toURI( table ), settings );
 		}
 		catch ( IOException e )

diff --git a/src/main/java/org/embl/mobie/command/open/OpenTableCommand.java b/src/main/java/org/embl/mobie/command/open/OpenTableCommand.java
@@ -60,9 +60,9 @@ public class OpenTableCommand implements Command {
 	@Parameter( label = "Labels Path Columns (Comma Separated)", required = false )
 	public String labels;
 
-	@Parameter( label = "Images & Labels Root Folder",
+	@Parameter( label = "Data Root Folder",
 			style = "directory",
-			description = "Use this is if the images and labels paths in the table are relative.",
+			description = "Use this is if the paths to the images and labels in the table are relative.",
 			required = false )
 	public File root;
 

diff --git a/src/main/java/org/embl/mobie/command/open/project/OpenMoBIEProjectCommand.java b/src/main/java/org/embl/mobie/command/open/project/OpenMoBIEProjectCommand.java
@@ -31,15 +31,12 @@
 import org.embl.mobie.MoBIE;
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
-import org.embl.mobie.lib.MoBIEHelper;
 import org.embl.mobie.lib.io.DataFormats;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 
 import java.io.IOException;
-import java.net.URI;
-import java.net.URL;
 
 
 @Plugin(type = Command.class, menuPath = CommandConstants.MOBIE_PLUGIN_OPEN_PROJECT + "Open MoBIE Project..." )

diff --git a/src/main/java/org/embl/mobie/command/open/project/OpenPlatyBrowserCommand.java b/src/main/java/org/embl/mobie/command/open/project/OpenPlatyBrowserCommand.java
@@ -49,7 +49,7 @@ public void run()
 
 		try
 		{
-			new MoBIE( "https://github.com/mobie/platybrowser-project", settings );
+			new MoBIE( "https://github.com/mobie/platybrowser-project",  settings );
 		}
 		catch ( IOException e )
 		{

diff --git a/src/main/java/org/embl/mobie/lib/ImageDataAdder.java b/src/main/java/org/embl/mobie/lib/ImageDataAdder.java
@@ -28,7 +28,6 @@
  */
 package org.embl.mobie.lib;
 
-import mpicbg.spim.data.generic.sequence.BasicViewSetup;
 import org.apache.commons.io.FilenameUtils;
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.io.ImageDataFormat;
@@ -44,8 +43,6 @@
 import org.embl.mobie.lib.serialize.display.SegmentationDisplay;
 import org.embl.mobie.lib.table.TableDataFormat;
 import org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata;
-import org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialDatasetMetadata;
-import spimdata.util.Displaysettings;
 
 import java.io.File;
 import java.util.Arrays;
@@ -110,7 +107,7 @@ private void addData( ImageData< ? > imageData, boolean isSegmentation )
 			}
 
 			dataSource.preInit( true );
-			dataset.addDataSource( dataSource );
+			dataset.putDataSource( dataSource );
 			dataset.is2D( MoBIEHelper.is2D( imageData, datasetIndex ) );
 		}
 	}

diff --git a/src/main/java/org/embl/mobie/lib/annotation/DefaultAnnotationAdapter.java b/src/main/java/org/embl/mobie/lib/annotation/DefaultAnnotationAdapter.java
@@ -32,30 +32,39 @@
 
 import java.util.Iterator;
 import java.util.Map;
-import java.util.Set;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.atomic.AtomicBoolean;
-import java.util.stream.Collectors;
 
 public class DefaultAnnotationAdapter< A extends Annotation > implements AnnotationAdapter< A >
 {
 	private final AtomicBoolean throwError = new AtomicBoolean( true );
 	private final AnnData< A > annData;
 	private final String source;
+	private final A annotation;
 	private Map< String, A > stlToAnnotation; // source, timepoint, label
 
 	public DefaultAnnotationAdapter( AnnData< A > annData )
 	{
 		this.annData = annData;
 		this.source = null;
+		this.annotation = null;
 	}
 
 	public DefaultAnnotationAdapter( AnnData< A > annData, String source )
 	{
 		this.annData = annData;
 		this.source = source;
+		this.annotation = null;
 	}
 
+	public DefaultAnnotationAdapter( AnnData< A > annData, String source, A annotation )
+	{
+		this.annData = annData;
+		this.source = source;
+		this.annotation = annotation;
+	}
+
+	// FIXME: Can we get rid of this? Currently not used...
 	@Override
 	public A createVariable()
 	{
@@ -87,6 +96,7 @@ public synchronized A getAnnotation( String source, final int timePoint, final i
 
 		if ( annotation == null )
 		{
+			// FIXME: Check whether this could be done lazy?
 			if ( throwError.get() )
 			{
 				System.err.println( "AnnotationAdapter: Missing annotation: " + source+ "; time point = " + timePoint + "; label = " + label + "\nSuppressing further errors of that kind." );

diff --git a/src/main/java/org/embl/mobie/lib/bdv/MobieBdvSupplier.java b/src/main/java/org/embl/mobie/lib/bdv/MobieBdvSupplier.java
@@ -91,7 +91,7 @@ public BdvHandle get()
         JFrame bdvFrame = (JFrame) SwingUtilities.getWindowAncestor(bdvHandle.getViewerPanel());
 
         // Get the existing menu bar
-        // Here we could add or remove stuff...
+        // TODO: Here we could add or remove stuff...
         JMenuBar menuBar = bdvFrame.getJMenuBar();
 
         setTimepointTextColor( bdvHandle );

diff --git a/src/main/java/org/embl/mobie/lib/data/CollectionTableDataSetter.java b/src/main/java/org/embl/mobie/lib/data/CollectionTableDataSetter.java
@@ -31,10 +31,12 @@
 public class CollectionTableDataSetter
 {
     private final Table table;
+    private final String rootPath;
 
-    public CollectionTableDataSetter( Table table )
+    public CollectionTableDataSetter( Table table, String rootPath )
     {
         this.table = table;
+        this.rootPath = rootPath;
     }
 
     public void addToDataset( Dataset dataset )
@@ -45,10 +47,12 @@ public void addToDataset( Dataset dataset )
         for ( Row row : table )
         {
             final StorageLocation storageLocation = new StorageLocation();
+
             storageLocation.absolutePath = getUri( row );
+            if ( rootPath != null )
+                storageLocation.absolutePath = IOHelper.combinePath( rootPath, storageLocation.absolutePath );
+
             ImageDataFormat imageDataFormat = ImageDataFormat.fromPath( storageLocation.absolutePath );
-            // FIXME: how to decide?
-            //imageDataFormat = ImageDataFormat.BioFormats;
             storageLocation.setChannel( getChannel( row ) ); // TODO: Fetch from table or URI? https://forum.image.sc/t/loading-only-one-channel-from-an-ome-zarr/97798
             String imageName = getName( row );
             String pixelType = getPixelType( row );
@@ -65,7 +69,7 @@ public void addToDataset( Dataset dataset )
                         );
 
                 segmentationDataSource.preInit( false );
-                dataset.addDataSource( segmentationDataSource );
+                dataset.putDataSource( segmentationDataSource );
 
                 display = createSegmentationDisplay(
                         imageName,
@@ -75,7 +79,7 @@ public void addToDataset( Dataset dataset )
             {
                 final ImageDataSource imageDataSource = new ImageDataSource( imageName, imageDataFormat, storageLocation );
                 imageDataSource.preInit( false );
-                dataset.addDataSource( imageDataSource );
+                dataset.putDataSource( imageDataSource );
 
                 display = createImageDisplay(
                         imageName,
@@ -84,7 +88,8 @@ public void addToDataset( Dataset dataset )
 
             addDisplayToViews( dataset, display, row );
 
-            IJ.log("## " + imageName );
+            IJ.log(" " );
+            IJ.log("Name: " + imageName );
             IJ.log("URI: " + storageLocation.absolutePath );
             IJ.log("Opener: " + imageDataFormat );
             IJ.log("Type: " + pixelType );
@@ -147,7 +152,7 @@ private static void addDisplayToViews( Dataset dataset, Display< ? > display, Ro
         {
             final View newView = new View(
                     viewName,
-                    getGroup( display ),
+                    getGroup( display, row ),
                     displays,
                     transforms, // asserting that display name == image name
                     null,
@@ -160,10 +165,21 @@ private static void addDisplayToViews( Dataset dataset, Display< ? > display, Ro
     }
 
     @NotNull
-    private static String getGroup( Display< ? > display )
+    private static String getGroup( Display< ? > display, Row row )
     {
-        // TODO: fetch from table
-        return "views";
+        try
+        {
+            String name = row.getString( CollectionTableConstants.GROUP );
+
+            if ( name.isEmpty() )
+                return "views";
+
+            return name;
+        }
+        catch ( Exception e )
+        {
+            return "views";
+        }
     }
 
     private static String getViewName( Display< ? > display, Row row )

diff --git a/src/main/java/org/embl/mobie/lib/data/GridSourcesDataSetter.java b/src/main/java/org/embl/mobie/lib/data/GridSourcesDataSetter.java
@@ -103,13 +103,13 @@ public void addDataAndDisplaysAndViews( Dataset dataset )
 					final TableSource tableSource = ( ( LabelGridSources ) sources ).getLabelTable( imageName );
 					SegmentationDataSource segmentationDataSource = SegmentationDataSource.create( imageName, imageDataFormat, storageLocation, tableSource );
 					segmentationDataSource.preInit( false );
-					dataset.addDataSource( segmentationDataSource );
+					dataset.putDataSource( segmentationDataSource );
 				}
 				else
 				{
 					final ImageDataSource imageDataSource = new ImageDataSource( imageName, imageDataFormat, storageLocation );
 					imageDataSource.preInit( false );
-					dataset.addDataSource( imageDataSource );
+					dataset.putDataSource( imageDataSource );
 				}
 			}
 		}

diff --git a/src/main/java/org/embl/mobie/lib/hcs/HCSPlateAdder.java b/src/main/java/org/embl/mobie/lib/hcs/HCSPlateAdder.java
@@ -145,7 +145,7 @@ public void addPlateToDataset( Dataset dataset )
 						//
 						String siteID = getSiteID( plate, channel, well, site );
 						ImageDataSource imageDataSource = createImageDataSource( channel, site, siteID );
-						dataset.addDataSource( imageDataSource );
+						dataset.putDataSource( imageDataSource );
 
 						// add site image source to site grid
 						siteGrid.sources.add( imageDataSource.getName() );
@@ -166,7 +166,7 @@ public void addPlateToDataset( Dataset dataset )
 						// the one site is the well
 						//
 						ImageDataSource imageDataSource = createImageDataSource( channel, site, wellID );
-						dataset.addDataSource( imageDataSource );
+						dataset.putDataSource( imageDataSource );
 					}
 				}
 

diff --git a/src/main/java/org/embl/mobie/lib/image/AnnotationLabelImage.java b/src/main/java/org/embl/mobie/lib/image/AnnotationLabelImage.java
@@ -30,9 +30,11 @@
 
 import net.imglib2.type.numeric.IntegerType;
 import org.embl.mobie.lib.annotation.Annotation;
+import org.embl.mobie.lib.annotation.AnnotationAdapter;
 
 public interface AnnotationLabelImage< A extends Annotation > extends AnnotationImage< A >
 {
-	// Label image corresponding to {@code annotation.label()}
 	Image< ? extends IntegerType< ? > > getLabelImage();
+
+	AnnotationAdapter< A > getAnnotationAdapter();
 }
diff --git a/src/main/java/org/embl/mobie/lib/image/DefaultAnnotationLabelImage.java b/src/main/java/org/embl/mobie/lib/image/DefaultAnnotationLabelImage.java
@@ -119,4 +119,9 @@ public AnnData< A > getAnnData()
 		return labelImage;
 	}
 
+	@Override
+	public AnnotationAdapter< A > getAnnotationAdapter()
+	{
+		return annotationAdapter;
+	}
 }